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Thinh Nguyen
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Merge pull request #97 from ttngu207/no-curation
pull from main - add QC
2 parents a738ee7 + 10d12a6 commit 03e2d5f

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‎.github/workflows/development.yaml

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name: Development
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on:
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pull_request:
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push:
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branches:
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- '**' # every branch
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- '!gh-pages' # exclude gh-pages branch
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- '!stage*' # exclude branches beginning with stage
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tags:
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- '*.*.*'
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- '\d+\.\d+\.\d+' # only semver tags
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pull_request:
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branches:
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- '**' # every branch
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- '!gh-pages' # exclude gh-pages branch
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- '!stage*' # exclude branches beginning with stage
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jobs:
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test-changelog:
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runs-on: ubuntu-latest
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uses: actions/upload-artifact@v2
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with:
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name: image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-${{matrix.distro}}
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path: "image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-\
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path:
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"image-${{env.PKG_NAME}}-${{env.PKG_VERSION}}-py${{matrix.py_ver}}-\
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${{matrix.distro}}.tar.gz"
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retention-days: 1
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- if: matrix.py_ver == '3.8' && matrix.distro == 'alpine'
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path: dist
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retention-days: 1
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publish-release:
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if: github.event_name == 'push'
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if: |
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github.event_name == 'push' &&
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startsWith(github.ref, 'refs/tags')
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needs: build
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runs-on: ubuntu-latest
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env:
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asset_path: ${{env.PKG_SDIST_PATH}}
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asset_name: pip-${{env.SDIST_PKG_NAME}}-${{env.PKG_VERSION}}.tar.gz
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asset_content_type: application/gzip
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publish-docs:
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if: |
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github.event_name == 'push' &&
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startsWith(github.ref, 'refs/tags')
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needs: build
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runs-on: ubuntu-latest
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env:
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DOCKER_CLIENT_TIMEOUT: "120"
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COMPOSE_HTTP_TIMEOUT: "120"
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steps:
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- uses: actions/checkout@v2
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- name: Deploy docs
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run: |
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export MODE=BUILD
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export PACKAGE=element_array_ephys
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export UPSTREAM_REPO=https://github.com/${GITHUB_REPOSITORY}.git
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export HOST_UID=$(id -u)
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docker compose -f docs/docker-compose.yaml up --exit-code-from docs --build
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git push origin gh-pages

‎.github/workflows/u24_element_before_release.yml

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name: u24_element_before_release
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on:
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pull_request:
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push:
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branches:
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- '**'
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tags-ignore:
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- '**'
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workflow_dispatch:
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jobs:
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call_context_check:
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uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
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call_u24_elements_build_alpine:
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uses: dj-sciops/djsciops-cicd/.github/workflows/u24_element_build.yaml@main
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with:
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py_ver: 3.9
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image: djbase

‎.github/workflows/u24_element_release_call.yml

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name: u24_element_release_call
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on:
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workflow_run:
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workflows: ["u24_element_tag_to_release"]
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types:
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- completed
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jobs:
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call_context_check:
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uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
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test_call_u24_elements_release_alpine:
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if: >-
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github.event.workflow_run.conclusion == 'success' && ( contains(github.event.workflow_run.head_branch, 'test') || (github.event.workflow_run.event == 'pull_request'))
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uses: dj-sciops/djsciops-cicd/.github/workflows/u24_element_release.yaml@main
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with:
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py_ver: 3.9
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twine_repo: testpypi
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secrets:
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TWINE_USERNAME: ${{secrets.TWINE_TEST_USERNAME}}
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TWINE_PASSWORD: ${{secrets.TWINE_TEST_PASSWORD}}
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call_u24_elements_release_alpine:
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if: >-
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github.event.workflow_run.conclusion == 'success' && github.repository_owner == 'datajoint' && !contains(github.event.workflow_run.head_branch, 'test')
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uses: dj-sciops/djsciops-cicd/.github/workflows/u24_element_release.yaml@main
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with:
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py_ver: 3.9
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secrets:
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TWINE_USERNAME: ${{secrets.TWINE_USERNAME}}
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TWINE_PASSWORD: ${{secrets.TWINE_PASSWORD}}

‎.github/workflows/u24_element_tag_to_release.yml

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name: u24_element_tag_to_release
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on:
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push:
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tags:
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- '*.*.*'
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- 'test*.*.*'
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jobs:
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call_context_check:
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uses: dj-sciops/djsciops-cicd/.github/workflows/context_check.yaml@main
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call_u24_elements_build_alpine:
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uses: dj-sciops/djsciops-cicd/.github/workflows/u24_element_build.yaml@main
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with:
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py_ver: 3.9
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image: djbase

‎.gitignore

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.ropeproject
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# mkdocs documentation
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/site
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docs/site
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# mypy
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.mypy_cache/
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**/#*#
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**/.#*
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docker-compose.y*ml
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docker-compose.y*ml
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# include
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!docs/docker-compose.yaml

‎CHANGELOG.md

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# Changelog
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Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
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Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
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[Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
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## [0.1.5] - 2022-07-11
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+ Add - New `QualityMetrics` table to store clusters' and waveforms' metrics after the spike sorting analysis.
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## [0.1.4] - 2022-07-11
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+ Bugfix - Handle case where `spike_depths` data is present.
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## [0.1.3] - 2022-06-16
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+ Update - Allow for the `precluster_output_dir` attribute to be nullable when no pre-clustering is performed.
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## [0.1.2] - 2022-06-09
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+ Bugfix - Handle case where `pc_features.npy` does not exist.
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## [0.1.1] - 2022-06-01
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+ Add - Secondary attributes to `PreClusterParamSteps` table
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## [0.1.0] - 2022-05-26
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+ Update - Rename module for acute probe insertions from `ephys.py` to `ephys_acute.py`.
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+ Add - Module for pre-clustering steps (`ephys_precluster.py`), which is built off of `ephys_acute.py`.
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+ Add - Module for chronic probe insertions (`ephys_chronic.py`).
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+ Bugfix - Missing `fileTimeSecs` key in SpikeGLX meta file.
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+ Update - Move common functions to `element-interface` package.
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+ Add - NWB export function
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## [0.1.0b4] - 2021-11-29
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### Added
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+ Processing with Kilosort and pyKilosort for Open Ephys and SpikeGLX
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## [0.1.0b0] - 2021-05-07
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### Added
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+ First beta release
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+ Update - First beta release
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## [0.1.0a5] - 2021-05-05
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### Added
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+ Added GitHub Action release process
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+ `probe` and `ephys` elements
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+ Readers for: `SpikeGLX`, `Open Ephys`, `Kilosort`
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+ Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS, 2.0 - MS
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+ Add - GitHub Action release process
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+ Add - `probe` and `ephys` elements
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+ Add - Readers for: `SpikeGLX`, `Open Ephys`, `Kilosort`
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+ Add - Probe table supporting: Neuropixels probes 1.0 - 3A, 1.0 - 3B, 2.0 - SS, 2.0 - MS
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[0.1.4]: https://github.com/datajoint/element-array-ephys/compare/0.1.3...0.1.4
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[0.1.3]: https://github.com/datajoint/element-array-ephys/compare/0.1.2...0.1.3
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[0.1.2]: https://github.com/datajoint/element-array-ephys/compare/0.1.1...0.1.2
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[0.1.1]: https://github.com/datajoint/element-array-ephys/compare/0.1.0...0.1.1
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[0.1.0]: https://github.com/datajoint/element-array-ephys/compare/0.1.0b0...0.1.0
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[0.1.0b0]: https://github.com/datajoint/element-array-ephys/compare/0.1.0a5...0.1.0b0
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[0.1.0a5]: https://github.com/datajoint/element-array-ephys/releases/tag/0.1.0a5

‎README.md

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## Element architecture
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![element-array-ephys diagram](images/attached_array_ephys_element.svg)
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`element-array-ephys` is comprised of two schemas, `probe` and `ephys`. To handle
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several use cases of this pipeline, we have designed several `ephys` schemas, including
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`ephys_acute`, `ephys_chronic`, and `ephys_precluster`.
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+ `ephys_acute` - A probe(s) is inserted into a new location during each session.
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+ `ephys_chronic` - A probe(s) is inserted once and used to record across multiple
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sessions.
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+ `ephys_precluster` - A probe(s) is inserted into a new location during each session.
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And pre-clustering steps (e.g. CatGT) are performed on the data from each probe prior
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to Kilosort analysis.
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### `ephys_acute` module
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![element-array-ephys acute diagram](images/attached_array_ephys_element_acute.svg)
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### `ephys_chronic` module
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![element-array-ephys chronic diagram](images/attached_array_ephys_element_chronic.svg)
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### `ephys_precluster` module
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![element-array-ephys precluster diagram](
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images/attached_array_ephys_element_precluster.svg)
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As the diagram depicts, the array ephys element starts immediately downstream from `Session`,
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and also requires some notion of `Location` as a dependency for `InsertionLocation`. We

‎docs/.docker/Dockerfile

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FROM datajoint/miniconda3:4.10.3-py3.9-alpine
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ARG PACKAGE
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WORKDIR /main
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COPY --chown=anaconda:anaconda ./docs/.docker/apk_requirements.txt ${APK_REQUIREMENTS}
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COPY --chown=anaconda:anaconda ./docs/.docker/pip_requirements.txt ${PIP_REQUIREMENTS}
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RUN \
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/entrypoint.sh echo "Dependencies installed" && \
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git config --global user.name "GitHub Action" && \
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git config --global user.email "action@github.com"&& \
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git config --global pull.rebase false && \
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git init
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COPY --chown=anaconda:anaconda ./${PACKAGE} /main/${PACKAGE}
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COPY --chown=anaconda:anaconda ./docs/mkdocs.yaml /main/docs/mkdocs.yaml
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COPY --chown=anaconda:anaconda ./docs/src /main/docs/src
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COPY --chown=anaconda:anaconda ./CHANGELOG.md /main/docs/src/about/changelog.md

‎docs/.docker/apk_requirements.txt

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git

‎docs/.docker/pip_requirements.txt

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mkdocs-material
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mkdocs-redirects
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mkdocstrings
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mkdocstrings-python
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mike
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mdx-truly-sane-lists
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mkdocs-gen-files
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mkdocs-literate-nav
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mkdocs-exclude-search

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